Starting phenix.real_space_refine
on Sun May 11 17:29:45 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8jlc_36392/05_2025/8jlc_36392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlc_36392/05_2025/8jlc_36392.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlc_36392/05_2025/8jlc_36392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlc_36392/05_2025/8jlc_36392.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlc_36392/05_2025/8jlc_36392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlc_36392/05_2025/8jlc_36392.cif"
  }
  resolution = 2.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    5291      2.51       5
     N    1362      2.21       5
     O    1489      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8189
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4674
          Classifications: {'peptide': 592}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 576}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3437
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411}
    Chain: "F"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 40
          Unusual residues: {'NAG': 2, 'UKX': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.20, per 1000 atoms: 0.63
  Number of scatterers: 8189
  At special positions: 0
  Unit cell: (87.98, 85.49, 147.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1489      8.00
     N    1362      7.00
     C    5291      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
    BETA1-6
      " NAG F   1 " - " FUC F   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 801 " - " ASN A 498 "
      " NAG A 802 " - " ASN A 548 "
      " NAG F   1 " - " ASN A 573 "
  Time building additional restraints: 2.17
  Conformation dependent library (CDL) restraints added in 960.9 milliseconds
  

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1866

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 7 sheets defined
      44.9% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 137 through 160
    Processing helix  chain 'A' and resid 162 through 183
      removed outlier: 4.099A  pdb=" N   ASP A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   VAL A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 197
      Proline residue:  A 191  - end of helix
      removed outlier: 4.316A  pdb=" N   LYS A 195 " --> pdb=" O   PRO A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 209
    Processing helix  chain 'A' and resid 209 through 230
      removed outlier: 3.965A  pdb=" N   LEU A 213 " --> pdb=" O   LEU A 209 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   MET A 215 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE A 220 " --> pdb=" O   MET A 216 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ASP A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ARG A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 252
      removed outlier: 3.911A  pdb=" N   PHE A 251 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 271
      removed outlier: 4.319A  pdb=" N   GLY A 271 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 281
      removed outlier: 3.525A  pdb=" N   ILE A 275 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 284
      No H-bonds generated for 'chain 'A' and resid 282 through 284'
    Processing helix  chain 'A' and resid 285 through 288
      removed outlier: 3.766A  pdb=" N   LYS A 288 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 285 through 288'
    Processing helix  chain 'A' and resid 289 through 295
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.802A  pdb=" N   MET A 301 " --> pdb=" O   CYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.754A  pdb=" N   VAL A 335 " --> pdb=" O   HIS A 331 " (cutoff:3.500A)
      Proline residue:  A 343  - end of helix
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 3.577A  pdb=" N   PHE A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 386
    Processing helix  chain 'A' and resid 419 through 439
    Processing helix  chain 'A' and resid 444 through 483
      Proline residue:  A 469  - end of helix
    Processing helix  chain 'A' and resid 562 through 564
      No H-bonds generated for 'chain 'A' and resid 562 through 564'
    Processing helix  chain 'A' and resid 593 through 623
      Proline residue:  A 610  - end of helix
      removed outlier: 5.245A  pdb=" N   ASP A 620 " --> pdb=" O   ALA A 616 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   LYS A 621 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 641
      removed outlier: 3.678A  pdb=" N   MET A 634 " --> pdb=" O   GLY A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 644
      No H-bonds generated for 'chain 'A' and resid 642 through 644'
    Processing helix  chain 'A' and resid 647 through 676
      removed outlier: 3.720A  pdb=" N   ILE A 663 " --> pdb=" O   GLY A 659 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   ALA A 664 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   SER A 665 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 707
      removed outlier: 3.567A  pdb=" N   PHE A 707 " --> pdb=" O   ILE A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 731
    Processing helix  chain 'B' and resid 929 through 933
      removed outlier: 3.760A  pdb=" N   VAL B 933 " --> pdb=" O   ASN B 930 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 954 through 958
    Processing helix  chain 'B' and resid 1080 through 1092
    Processing helix  chain 'B' and resid 1210 through 1215
      removed outlier: 4.235A  pdb=" N   VAL B1214 " --> pdb=" O   ILE B1211 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   GLY B1215 " --> pdb=" O   PRO B1212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1265 through 1273
    Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 485 through 492
    current: chain 'A' and resid 515 through 527
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 515 through 527
    current: chain 'B' and resid 1142 through 1144
    Processing sheet with id=AA2, first strand: chain 'B' and resid 877 through 884
      removed outlier: 3.590A  pdb=" N   ASP B 887 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 887 through 890
    current: chain 'B' and resid 914 through 916
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 914 through 916
    current: chain 'B' and resid 1015 through 1021
      removed outlier: 4.000A  pdb=" N   ASP B1037 " --> pdb=" O   ILE B1029 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ILE B1031 " --> pdb=" O   LEU B1035 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   LEU B1035 " --> pdb=" O   ILE B1031 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 897 through 900
    Processing sheet with id=AA4, first strand: chain 'B' and resid 962 through 966
      removed outlier: 6.724A  pdb=" N   VAL B 976 " --> pdb=" O   ILE B 964 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ASN B 966 " --> pdb=" O   TRP B 974 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   TRP B 974 " --> pdb=" O   ASN B 966 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1112 through 1115
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1122 through 1124
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1159 through 1164
      removed outlier: 4.119A  pdb=" N   LYS B1159 " --> pdb=" O   VAL B1185 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   ILE B1182 " --> pdb=" O   LEU B1193 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 1189 through 1194
    current: chain 'B' and resid 1232 through 1240
      removed outlier: 27.387A  pdb=" N   ASN B1233 " --> pdb=" O   LEU B1254 " (cutoff:3.500A)
      removed outlier: 23.558A  pdb=" N   LEU B1254 " --> pdb=" O   ASN B1233 " (cutoff:3.500A)
      removed outlier: 15.950A  pdb=" N   CYS B1235 " --> pdb=" O   PHE B1252 " (cutoff:3.500A)
      removed outlier: 11.246A  pdb=" N   PHE B1252 " --> pdb=" O   CYS B1235 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   MET B1237 " --> pdb=" O   ILE B1250 " (cutoff:3.500A)

    374 hydrogen bonds defined for protein.
    1077 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.27

  Time building geometry restraints manager: 2.51 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.33: 1771
        1.33 -     1.47: 3037
        1.47 -     1.61: 3497
        1.61 -     1.75: 3
        1.75 -     1.89: 75
  Bond restraints: 8383
  Sorted by residual:
  bond pdb=" C   GLY A 591 "
       pdb=" N   GLU A 592 "
    ideal  model  delta    sigma   weight residual
    1.335  1.458 -0.123 1.35e-02 5.49e+03 8.37e+01
  bond pdb=" C5  UKX A 803 "
       pdb=" C6  UKX A 803 "
    ideal  model  delta    sigma   weight residual
    1.533  1.709 -0.176 2.00e-02 2.50e+03 7.78e+01
  bond pdb=" C   GLY A 604 "
       pdb=" O   GLY A 604 "
    ideal  model  delta    sigma   weight residual
    1.233  1.290 -0.057 1.17e-02 7.31e+03 2.40e+01
  bond pdb=" N   GLU A 592 "
       pdb=" CA  GLU A 592 "
    ideal  model  delta    sigma   weight residual
    1.458  1.517 -0.059 1.30e-02 5.92e+03 2.07e+01
  bond pdb=" C   VAL A 171 "
       pdb=" O   VAL A 171 "
    ideal  model  delta    sigma   weight residual
    1.237  1.285 -0.048 1.13e-02 7.83e+03 1.82e+01
  ... (remaining 8378 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.17: 11091
        3.17 -     6.35: 231
        6.35 -     9.52: 11
        9.52 -    12.69: 1
       12.69 -    15.87: 1
  Bond angle restraints: 11335
  Sorted by residual:
  angle pdb=" C   GLY A 591 "
        pdb=" N   GLU A 592 "
        pdb=" CA  GLU A 592 "
      ideal   model   delta    sigma   weight residual
     120.60  136.47  -15.87 1.60e+00 3.91e-01 9.84e+01
  angle pdb=" OD1 ASN A 498 "
        pdb=" CG  ASN A 498 "
        pdb=" ND2 ASN A 498 "
      ideal   model   delta    sigma   weight residual
     122.60  116.64    5.96 1.00e+00 1.00e+00 3.55e+01
  angle pdb=" N   VAL A 671 "
        pdb=" CA  VAL A 671 "
        pdb=" C   VAL A 671 "
      ideal   model   delta    sigma   weight residual
     110.62  115.27   -4.65 1.02e+00 9.61e-01 2.08e+01
  angle pdb=" CA  ASP B1256 "
        pdb=" CB  ASP B1256 "
        pdb=" CG  ASP B1256 "
      ideal   model   delta    sigma   weight residual
     112.60  117.08   -4.48 1.00e+00 1.00e+00 2.01e+01
  angle pdb=" N   ILE B1148 "
        pdb=" CA  ILE B1148 "
        pdb=" C   ILE B1148 "
      ideal   model   delta    sigma   weight residual
     111.62  108.13    3.49 7.90e-01 1.60e+00 1.95e+01
  ... (remaining 11330 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.69: 4439
       15.69 -    31.38: 423
       31.38 -    47.07: 75
       47.07 -    62.76: 15
       62.76 -    78.45: 12
  Dihedral angle restraints: 4964
    sinusoidal: 2041
      harmonic: 2923
  Sorted by residual:
  dihedral pdb=" CA  ILE B1053 "
           pdb=" C   ILE B1053 "
           pdb=" N   MET B1054 "
           pdb=" CA  MET B1054 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.88  -28.12     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  GLU B1210 "
           pdb=" C   GLU B1210 "
           pdb=" N   ILE B1211 "
           pdb=" CA  ILE B1211 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.43  -20.57     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  PHE A 497 "
           pdb=" C   PHE A 497 "
           pdb=" N   ASN A 498 "
           pdb=" CA  ASN A 498 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.23   19.77     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 4961 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.252: 1237
       0.252 -    0.504: 6
       0.504 -    0.755: 0
       0.755 -    1.007: 0
       1.007 -    1.259: 1
  Chirality restraints: 1244
  Sorted by residual:
  chirality pdb=" C1  FUC F   3 "
            pdb=" O6  NAG F   1 "
            pdb=" C2  FUC F   3 "
            pdb=" O5  FUC F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-02 2.50e+03 5.32e+01
  chirality pdb=" C1  NAG A 801 "
            pdb=" ND2 ASN A 498 "
            pdb=" C2  NAG A 801 "
            pdb=" O5  NAG A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.14   -1.26 2.00e-01 2.50e+01 3.96e+01
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.30   -0.10 2.00e-02 2.50e+03 2.67e+01
  ... (remaining 1241 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 467 "    0.067 2.00e-02 2.50e+03   5.61e-02 7.88e+01
        pdb=" CG  TRP A 467 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 467 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 467 "   -0.024 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 467 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 467 "    0.076 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 467 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 467 "    0.085 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 467 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 467 "   -0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 548 "    0.066 2.00e-02 2.50e+03   7.39e-02 6.82e+01
        pdb=" CG  ASN A 548 "   -0.019 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 548 "   -0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 548 "   -0.124 2.00e-02 2.50e+03
        pdb=" C1  NAG A 802 "    0.085 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 802 "   -0.073 2.00e-02 2.50e+03   6.05e-02 4.57e+01
        pdb=" C7  NAG A 802 "    0.019 2.00e-02 2.50e+03
        pdb=" C8  NAG A 802 "   -0.055 2.00e-02 2.50e+03
        pdb=" N2  NAG A 802 "    0.098 2.00e-02 2.50e+03
        pdb=" O7  NAG A 802 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 613
        2.74 -     3.28: 8249
        3.28 -     3.82: 13731
        3.82 -     4.36: 16864
        4.36 -     4.90: 28701
  Nonbonded interactions: 68158
  Sorted by model distance:
  nonbonded pdb=" O   TRP B1266 "
            pdb=" NE2 GLN B1270 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" OG1 THR B1195 "
            pdb=" O   ILE B1205 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OH  TYR A 279 "
            pdb=" O   PRO A 355 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NE2 GLN A 323 "
            pdb=" O   GLY A 325 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" OD1 ASP A 470 "
            pdb=" NH2 ARG A 473 "
     model   vdw
     2.288 3.120
  ... (remaining 68153 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.360
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6977
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.226   8388  Z= 0.678
  Angle     :  1.275  34.306  11350  Z= 0.791
  Chirality :  0.086   1.259   1244
  Planarity :  0.011   0.149   1428
  Dihedral  : 13.035  78.450   3098
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.26), residues: 1006
  helix:  1.06 (0.25), residues: 405
  sheet: -0.08 (0.33), residues: 241
  loop : -1.33 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.085   0.012   TRP A 467 
 HIS   0.013   0.004   HIS A 161 
 PHE   0.068   0.011   PHE A 299 
 TYR   0.053   0.009   TYR A 169 
 ARG   0.024   0.003   ARG B1140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.14410 (    3)
  link_NAG-ASN         : angle      16.76596 (    9)
  link_BETA1-4         : bond        0.00096 (    1)
  link_BETA1-4         : angle       1.68604 (    3)
  hydrogen bonds       : bond        0.13527 (  374)
  hydrogen bonds       : angle       5.89288 ( 1077)
  link_BETA1-6         : bond        0.01775 (    1)
  link_BETA1-6         : angle       1.37472 (    3)
  covalent geometry    : bond        0.01068 ( 8383)
  covalent geometry    : angle       1.18478 (11335)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ARG cc_start: 0.6366 (tpp80) cc_final: 0.5741 (mtp85)
REVERT: A  197 MET cc_start: 0.6566 (mtm) cc_final: 0.5263 (tpt)
REVERT: A  227 ASP cc_start: 0.8194 (m-30) cc_final: 0.7946 (m-30)
REVERT: A  366 LYS cc_start: 0.6546 (mtmt) cc_final: 0.6283 (mttm)
REVERT: A  372 MET cc_start: 0.7261 (mtm) cc_final: 0.7027 (mmm)
REVERT: A  444 ARG cc_start: 0.6477 (ttp-110) cc_final: 0.6245 (ttt180)
REVERT: A  491 ARG cc_start: 0.7519 (tmt170) cc_final: 0.7252 (tmt170)
REVERT: A  520 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7509 (tmm-80)
REVERT: A  542 SER cc_start: 0.8059 (t) cc_final: 0.7844 (t)
REVERT: A  563 GLU cc_start: 0.8138 (pt0) cc_final: 0.7196 (tp30)
REVERT: A  567 VAL cc_start: 0.7421 (t) cc_final: 0.7180 (t)
REVERT: A  568 ASN cc_start: 0.8211 (t0) cc_final: 0.7877 (p0)
REVERT: A  581 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7273 (mm-30)
REVERT: B  910 ASP cc_start: 0.5165 (t0) cc_final: 0.4352 (t0)
REVERT: B  925 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7527 (mm-30)
REVERT: B 1097 LEU cc_start: 0.6800 (mm) cc_final: 0.6475 (tt)
REVERT: B 1127 ASN cc_start: 0.8545 (m-40) cc_final: 0.8332 (p0)
REVERT: B 1203 GLU cc_start: 0.5470 (mt-10) cc_final: 0.4936 (mm-30)
REVERT: B 1219 GLN cc_start: 0.7566 (pt0) cc_final: 0.6767 (pt0)
REVERT: B 1246 ASP cc_start: 0.7038 (p0) cc_final: 0.6682 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 1.3062
  time to fit residues: 242.7517
Evaluate side-chains
  131 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0050
   chunk 91 optimal weight:    0.2980
   overall best weight:    0.5194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
A 434 ASN
A 513 ASN
B1073 ASN
B1115 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.223967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.145370 restraints weight = 8791.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.58
r_work: 0.3463 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8388  Z= 0.139
  Angle     :  0.616  14.106  11350  Z= 0.314
  Chirality :  0.046   0.473   1244
  Planarity :  0.003   0.034   1428
  Dihedral  :  6.235  56.778   1221
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  9.33 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.27), residues: 1006
  helix:  1.95 (0.25), residues: 408
  sheet:  0.12 (0.34), residues: 231
  loop : -1.17 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 300 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.017   0.001   PHE A 512 
 TYR   0.013   0.001   TYR A 306 
 ARG   0.005   0.001   ARG B 903 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00713 (    3)
  link_NAG-ASN         : angle       7.65156 (    9)
  link_BETA1-4         : bond        0.00633 (    1)
  link_BETA1-4         : angle       0.90212 (    3)
  hydrogen bonds       : bond        0.05267 (  374)
  hydrogen bonds       : angle       4.78916 ( 1077)
  link_BETA1-6         : bond        0.00647 (    1)
  link_BETA1-6         : angle       1.33596 (    3)
  covalent geometry    : bond        0.00293 ( 8383)
  covalent geometry    : angle       0.57736 (11335)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7807 (tm-30)
REVERT: A  197 MET cc_start: 0.6772 (mtm) cc_final: 0.6160 (ttm)
REVERT: A  366 LYS cc_start: 0.7353 (mtmt) cc_final: 0.6743 (mttm)
REVERT: A  372 MET cc_start: 0.7586 (mtm) cc_final: 0.6982 (mmm)
REVERT: A  379 ASP cc_start: 0.6234 (m-30) cc_final: 0.5957 (m-30)
REVERT: A  382 MET cc_start: 0.6837 (mmt) cc_final: 0.6612 (mmt)
REVERT: A  444 ARG cc_start: 0.6933 (ttp-110) cc_final: 0.6659 (ttt180)
REVERT: A  491 ARG cc_start: 0.7556 (tmt170) cc_final: 0.7253 (tpt-90)
REVERT: A  497 PHE cc_start: 0.7995 (m-80) cc_final: 0.7762 (m-10)
REVERT: A  522 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7456 (tppt)
REVERT: A  563 GLU cc_start: 0.8118 (pt0) cc_final: 0.7485 (tp30)
REVERT: A  567 VAL cc_start: 0.8556 (t) cc_final: 0.8178 (m)
REVERT: A  568 ASN cc_start: 0.8314 (t0) cc_final: 0.7976 (p0)
REVERT: A  581 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7112 (mm-30)
REVERT: B  903 ARG cc_start: 0.6152 (mmm-85) cc_final: 0.5825 (mmm-85)
REVERT: B  910 ASP cc_start: 0.5406 (t0) cc_final: 0.4776 (t0)
REVERT: B  913 GLN cc_start: 0.5840 (pt0) cc_final: 0.5545 (pt0)
REVERT: B  925 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7596 (mm-30)
REVERT: B  955 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7673 (ptmt)
REVERT: B 1064 ARG cc_start: 0.6151 (mtm-85) cc_final: 0.5950 (mtm-85)
REVERT: B 1175 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.6207 (mtm-85)
REVERT: B 1219 GLN cc_start: 0.7723 (pt0) cc_final: 0.7280 (pt0)
REVERT: B 1226 LYS cc_start: 0.7336 (pttm) cc_final: 0.6829 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7504 (p0) cc_final: 0.7166 (p0)
  outliers start: 20
  outliers final: 6
  residues processed: 153
  average time/residue: 1.2395
  time to fit residues: 201.7055
Evaluate side-chains
  136 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  522 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  955 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1175 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 93 optimal weight:   10.0000
   chunk 64 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 364 ASN
A 387 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.218730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.137218 restraints weight = 8920.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.67
r_work: 0.3433 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8388  Z= 0.182
  Angle     :  0.609  11.672  11350  Z= 0.312
  Chirality :  0.047   0.447   1244
  Planarity :  0.003   0.027   1428
  Dihedral  :  5.928  55.400   1221
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 12.74 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 1006
  helix:  1.87 (0.25), residues: 412
  sheet:  0.29 (0.33), residues: 228
  loop : -1.10 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B1266 
 HIS   0.005   0.001   HIS A 494 
 PHE   0.017   0.002   PHE A 516 
 TYR   0.018   0.001   TYR A 306 
 ARG   0.004   0.000   ARG B 903 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00561 (    3)
  link_NAG-ASN         : angle       6.06966 (    9)
  link_BETA1-4         : bond        0.00739 (    1)
  link_BETA1-4         : angle       0.93057 (    3)
  hydrogen bonds       : bond        0.05730 (  374)
  hydrogen bonds       : angle       4.69624 ( 1077)
  link_BETA1-6         : bond        0.00429 (    1)
  link_BETA1-6         : angle       1.22494 (    3)
  covalent geometry    : bond        0.00428 ( 8383)
  covalent geometry    : angle       0.58446 (11335)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7738 (tm-30)
REVERT: A  197 MET cc_start: 0.6558 (mtm) cc_final: 0.5080 (tpt)
REVERT: A  366 LYS cc_start: 0.7233 (mtmt) cc_final: 0.6589 (mttm)
REVERT: A  371 TRP cc_start: 0.7731 (t60) cc_final: 0.7490 (t60)
REVERT: A  372 MET cc_start: 0.7377 (mtm) cc_final: 0.6867 (mmm)
REVERT: A  379 ASP cc_start: 0.6195 (m-30) cc_final: 0.5892 (m-30)
REVERT: A  444 ARG cc_start: 0.6911 (ttp-110) cc_final: 0.6447 (ttt180)
REVERT: A  491 ARG cc_start: 0.7554 (tmt170) cc_final: 0.7061 (tpt-90)
REVERT: A  497 PHE cc_start: 0.7969 (m-80) cc_final: 0.7612 (m-10)
REVERT: A  522 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7430 (tppt)
REVERT: A  563 GLU cc_start: 0.8108 (pt0) cc_final: 0.7463 (tp30)
REVERT: A  567 VAL cc_start: 0.8490 (t) cc_final: 0.8032 (m)
REVERT: A  568 ASN cc_start: 0.8245 (t0) cc_final: 0.7836 (p0)
REVERT: A  581 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7091 (mm-30)
REVERT: A  742 GLN cc_start: 0.7029 (tm-30) cc_final: 0.6688 (tm-30)
REVERT: B  903 ARG cc_start: 0.6206 (mmm-85) cc_final: 0.5983 (mmm-85)
REVERT: B  910 ASP cc_start: 0.5452 (t0) cc_final: 0.4702 (t0)
REVERT: B  913 GLN cc_start: 0.5553 (pt0) cc_final: 0.5263 (pt0)
REVERT: B  925 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7635 (mm-30)
REVERT: B  947 ILE cc_start: 0.7987 (tt) cc_final: 0.7655 (tp)
REVERT: B  996 ARG cc_start: 0.6022 (mtp85) cc_final: 0.5691 (mtt180)
REVERT: B 1061 ARG cc_start: 0.6673 (mtm-85) cc_final: 0.5983 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6118 (mtm-85) cc_final: 0.5846 (mtm-85)
REVERT: B 1097 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.5958 (tt)
REVERT: B 1175 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.6012 (mtm-85)
REVERT: B 1226 LYS cc_start: 0.7401 (pttm) cc_final: 0.6887 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7576 (p0) cc_final: 0.7257 (p0)
  outliers start: 26
  outliers final: 11
  residues processed: 155
  average time/residue: 1.2097
  time to fit residues: 199.0393
Evaluate side-chains
  143 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  646 ASN
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1097 LEU
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0170
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.7018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 378 HIS
B 988 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.220715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.140225 restraints weight = 8846.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.62
r_work: 0.3470 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8388  Z= 0.131
  Angle     :  0.568   9.205  11350  Z= 0.290
  Chirality :  0.046   0.414   1244
  Planarity :  0.003   0.052   1428
  Dihedral  :  5.646  53.845   1221
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.24 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.27), residues: 1006
  helix:  2.03 (0.25), residues: 414
  sheet:  0.31 (0.34), residues: 227
  loop : -1.02 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B1266 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.019   0.001   PHE A 512 
 TYR   0.012   0.001   TYR A 306 
 ARG   0.004   0.000   ARG B1131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00494 (    3)
  link_NAG-ASN         : angle       4.80608 (    9)
  link_BETA1-4         : bond        0.00681 (    1)
  link_BETA1-4         : angle       0.87149 (    3)
  hydrogen bonds       : bond        0.04815 (  374)
  hydrogen bonds       : angle       4.45528 ( 1077)
  link_BETA1-6         : bond        0.00379 (    1)
  link_BETA1-6         : angle       1.07722 (    3)
  covalent geometry    : bond        0.00290 ( 8383)
  covalent geometry    : angle       0.55156 (11335)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6511 (mtm) cc_final: 0.5915 (ttm)
REVERT: A  227 ASP cc_start: 0.8315 (m-30) cc_final: 0.7909 (m-30)
REVERT: A  366 LYS cc_start: 0.7078 (mtmt) cc_final: 0.6468 (mttm)
REVERT: A  371 TRP cc_start: 0.7697 (t60) cc_final: 0.7423 (t60)
REVERT: A  372 MET cc_start: 0.7307 (mtm) cc_final: 0.6847 (mmp)
REVERT: A  379 ASP cc_start: 0.6098 (m-30) cc_final: 0.5855 (m-30)
REVERT: A  444 ARG cc_start: 0.6838 (ttp-110) cc_final: 0.6254 (ttt180)
REVERT: A  491 ARG cc_start: 0.7524 (tmt170) cc_final: 0.7023 (tpt-90)
REVERT: A  497 PHE cc_start: 0.7931 (m-80) cc_final: 0.7579 (m-10)
REVERT: A  522 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7423 (tppt)
REVERT: A  563 GLU cc_start: 0.8113 (pt0) cc_final: 0.7483 (tp30)
REVERT: A  567 VAL cc_start: 0.8453 (t) cc_final: 0.8019 (m)
REVERT: A  568 ASN cc_start: 0.8270 (t0) cc_final: 0.7859 (p0)
REVERT: A  581 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7144 (mm-30)
REVERT: A  742 GLN cc_start: 0.6977 (tm-30) cc_final: 0.6659 (tm-30)
REVERT: B  910 ASP cc_start: 0.5382 (t0) cc_final: 0.4606 (t0)
REVERT: B  913 GLN cc_start: 0.5528 (pt0) cc_final: 0.5172 (pt0)
REVERT: B  925 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7660 (mm-30)
REVERT: B  996 ARG cc_start: 0.6067 (mtp85) cc_final: 0.5717 (mtt180)
REVERT: B 1061 ARG cc_start: 0.6695 (mtm-85) cc_final: 0.5961 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6150 (mtm-85) cc_final: 0.5841 (mtm-85)
REVERT: B 1106 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6275 (mp10)
REVERT: B 1115 ASN cc_start: 0.7149 (m110) cc_final: 0.6856 (t0)
REVERT: B 1175 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6046 (mtm-85)
REVERT: B 1209 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5632 (pp)
REVERT: B 1219 GLN cc_start: 0.7177 (pt0) cc_final: 0.6713 (pt0)
REVERT: B 1226 LYS cc_start: 0.7480 (pttm) cc_final: 0.6869 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7569 (p0) cc_final: 0.7083 (p0)
REVERT: B 1282 TRP cc_start: 0.7452 (m100) cc_final: 0.7092 (m100)
  outliers start: 20
  outliers final: 10
  residues processed: 149
  average time/residue: 1.2456
  time to fit residues: 196.5722
Evaluate side-chains
  144 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  646 ASN
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1106 GLN
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 47 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 988 GLN
B1199 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.217159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.136505 restraints weight = 8845.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.59
r_work: 0.3416 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8388  Z= 0.191
  Angle     :  0.599   9.213  11350  Z= 0.309
  Chirality :  0.046   0.351   1244
  Planarity :  0.004   0.046   1428
  Dihedral  :  5.585  53.294   1221
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.04 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 1006
  helix:  1.83 (0.25), residues: 413
  sheet:  0.28 (0.34), residues: 227
  loop : -1.04 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 985 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.016   0.002   PHE A 516 
 TYR   0.018   0.002   TYR A 306 
 ARG   0.009   0.001   ARG A 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00421 (    3)
  link_NAG-ASN         : angle       4.35861 (    9)
  link_BETA1-4         : bond        0.00666 (    1)
  link_BETA1-4         : angle       0.99571 (    3)
  hydrogen bonds       : bond        0.05744 (  374)
  hydrogen bonds       : angle       4.60075 ( 1077)
  link_BETA1-6         : bond        0.00447 (    1)
  link_BETA1-6         : angle       1.22553 (    3)
  covalent geometry    : bond        0.00458 ( 8383)
  covalent geometry    : angle       0.58656 (11335)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6502 (mtm) cc_final: 0.5060 (tpt)
REVERT: A  366 LYS cc_start: 0.7222 (mtmt) cc_final: 0.6604 (mttm)
REVERT: A  371 TRP cc_start: 0.7756 (t60) cc_final: 0.7547 (t60)
REVERT: A  372 MET cc_start: 0.7319 (mtm) cc_final: 0.6869 (mmp)
REVERT: A  444 ARG cc_start: 0.6802 (ttp-110) cc_final: 0.6336 (ttt180)
REVERT: A  491 ARG cc_start: 0.7542 (tmt170) cc_final: 0.7136 (tpt-90)
REVERT: A  497 PHE cc_start: 0.7925 (m-80) cc_final: 0.7682 (m-10)
REVERT: A  522 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7456 (tppt)
REVERT: A  563 GLU cc_start: 0.8138 (pt0) cc_final: 0.7639 (tp30)
REVERT: A  567 VAL cc_start: 0.8502 (t) cc_final: 0.8254 (m)
REVERT: A  581 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7206 (mm-30)
REVERT: A  742 GLN cc_start: 0.6996 (tm-30) cc_final: 0.6720 (tm-30)
REVERT: B  910 ASP cc_start: 0.5301 (t0) cc_final: 0.4979 (t0)
REVERT: B  996 ARG cc_start: 0.6080 (mtp85) cc_final: 0.5768 (mtt180)
REVERT: B 1061 ARG cc_start: 0.6693 (mtm-85) cc_final: 0.5977 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6171 (mtm-85) cc_final: 0.5853 (mtm-85)
REVERT: B 1106 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6361 (mp10)
REVERT: B 1175 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6078 (mtm-85)
REVERT: B 1209 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5576 (pp)
REVERT: B 1226 LYS cc_start: 0.7428 (pttm) cc_final: 0.6871 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7578 (p0) cc_final: 0.7136 (p0)
REVERT: B 1265 ASN cc_start: 0.7824 (m-40) cc_final: 0.7584 (m110)
REVERT: B 1282 TRP cc_start: 0.7409 (m100) cc_final: 0.7051 (m100)
  outliers start: 24
  outliers final: 13
  residues processed: 147
  average time/residue: 1.2438
  time to fit residues: 193.6635
Evaluate side-chains
  140 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  465 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  646 ASN
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1106 GLN
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 61 optimal weight:    0.1980
   chunk 22 optimal weight:    0.5980
   chunk 76 optimal weight:   40.0000
   chunk 98 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0570
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.5100

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 988 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.221005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.140111 restraints weight = 8858.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.67
r_work: 0.3480 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8388  Z= 0.120
  Angle     :  0.554  10.478  11350  Z= 0.283
  Chirality :  0.043   0.320   1244
  Planarity :  0.003   0.046   1428
  Dihedral  :  5.281  49.546   1221
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.27 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.27), residues: 1006
  helix:  2.07 (0.25), residues: 417
  sheet:  0.28 (0.34), residues: 229
  loop : -1.03 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B1266 
 HIS   0.004   0.000   HIS A 494 
 PHE   0.018   0.001   PHE A 512 
 TYR   0.011   0.001   TYR A 306 
 ARG   0.008   0.000   ARG A 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00462 (    3)
  link_NAG-ASN         : angle       3.40243 (    9)
  link_BETA1-4         : bond        0.00731 (    1)
  link_BETA1-4         : angle       0.99920 (    3)
  hydrogen bonds       : bond        0.04477 (  374)
  hydrogen bonds       : angle       4.34947 ( 1077)
  link_BETA1-6         : bond        0.00469 (    1)
  link_BETA1-6         : angle       1.14122 (    3)
  covalent geometry    : bond        0.00261 ( 8383)
  covalent geometry    : angle       0.54519 (11335)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 GLU cc_start: 0.7801 (tp30) cc_final: 0.7311 (tp30)
REVERT: A  197 MET cc_start: 0.6409 (mtm) cc_final: 0.4931 (tpt)
REVERT: A  366 LYS cc_start: 0.6994 (mtmt) cc_final: 0.6410 (mttm)
REVERT: A  372 MET cc_start: 0.7306 (mtm) cc_final: 0.6861 (mmp)
REVERT: A  444 ARG cc_start: 0.6594 (ttp-110) cc_final: 0.6133 (ttt180)
REVERT: A  491 ARG cc_start: 0.7520 (tmt170) cc_final: 0.6954 (tpt-90)
REVERT: A  497 PHE cc_start: 0.7996 (m-80) cc_final: 0.7768 (m-10)
REVERT: A  522 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7444 (tppt)
REVERT: A  563 GLU cc_start: 0.8103 (pt0) cc_final: 0.7506 (tp30)
REVERT: A  567 VAL cc_start: 0.8443 (t) cc_final: 0.8233 (m)
REVERT: A  581 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7238 (mm-30)
REVERT: A  742 GLN cc_start: 0.6877 (tm-30) cc_final: 0.6631 (tm-30)
REVERT: B  910 ASP cc_start: 0.5337 (t0) cc_final: 0.4560 (t0)
REVERT: B  913 GLN cc_start: 0.5386 (pt0) cc_final: 0.4868 (pt0)
REVERT: B  996 ARG cc_start: 0.5990 (mtp85) cc_final: 0.5744 (mtt180)
REVERT: B 1061 ARG cc_start: 0.6687 (mtm-85) cc_final: 0.5947 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6188 (mtm-85) cc_final: 0.5861 (mtm-85)
REVERT: B 1106 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6313 (mp10)
REVERT: B 1133 TYR cc_start: 0.5668 (p90) cc_final: 0.5313 (p90)
REVERT: B 1175 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.6003 (mtm-85)
REVERT: B 1193 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5879 (mm)
REVERT: B 1209 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5658 (pp)
REVERT: B 1226 LYS cc_start: 0.7416 (pttm) cc_final: 0.6859 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7429 (p0) cc_final: 0.7000 (p0)
REVERT: B 1265 ASN cc_start: 0.7843 (m-40) cc_final: 0.7636 (m110)
REVERT: B 1282 TRP cc_start: 0.7270 (m100) cc_final: 0.6798 (m100)
  outliers start: 25
  outliers final: 11
  residues processed: 146
  average time/residue: 1.2044
  time to fit residues: 186.5644
Evaluate side-chains
  143 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  522 LYS
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  646 ASN
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1106 GLN
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1193 LEU
Chi-restraints excluded: chain B residue 1209 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 93 optimal weight:   20.0000
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0370
   chunk 79 optimal weight:    8.9990
   chunk 64 optimal weight:   20.0000
   chunk 90 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.9060

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 667 ASN
A 742 GLN
B 988 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.220439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.140598 restraints weight = 8863.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.57
r_work: 0.3486 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8388  Z= 0.146
  Angle     :  0.570  11.330  11350  Z= 0.295
  Chirality :  0.044   0.286   1244
  Planarity :  0.003   0.032   1428
  Dihedral  :  5.092  45.324   1221
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.41 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.27), residues: 1006
  helix:  2.09 (0.25), residues: 415
  sheet:  0.23 (0.34), residues: 224
  loop : -1.08 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B1266 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.018   0.001   PHE A 516 
 TYR   0.014   0.001   TYR A 306 
 ARG   0.007   0.000   ARG B 903 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00402 (    3)
  link_NAG-ASN         : angle       3.12485 (    9)
  link_BETA1-4         : bond        0.00655 (    1)
  link_BETA1-4         : angle       1.15149 (    3)
  hydrogen bonds       : bond        0.05063 (  374)
  hydrogen bonds       : angle       4.43414 ( 1077)
  link_BETA1-6         : bond        0.00451 (    1)
  link_BETA1-6         : angle       1.16486 (    3)
  covalent geometry    : bond        0.00332 ( 8383)
  covalent geometry    : angle       0.56294 (11335)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ARG cc_start: 0.7472 (ttp-110) cc_final: 0.7249 (mtm110)
REVERT: A  197 MET cc_start: 0.6602 (mtm) cc_final: 0.5066 (tpt)
REVERT: A  366 LYS cc_start: 0.7304 (mtmt) cc_final: 0.6668 (mttm)
REVERT: A  372 MET cc_start: 0.7542 (mtm) cc_final: 0.7070 (mmp)
REVERT: A  444 ARG cc_start: 0.6960 (ttp-110) cc_final: 0.6468 (ttt180)
REVERT: A  491 ARG cc_start: 0.7477 (tmt170) cc_final: 0.7066 (tpt-90)
REVERT: A  522 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7562 (tppt)
REVERT: A  535 TYR cc_start: 0.8608 (t80) cc_final: 0.8348 (t80)
REVERT: A  563 GLU cc_start: 0.8166 (pt0) cc_final: 0.7744 (tp30)
REVERT: A  567 VAL cc_start: 0.8690 (t) cc_final: 0.8487 (m)
REVERT: A  581 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7344 (mm-30)
REVERT: A  742 GLN cc_start: 0.7105 (tm130) cc_final: 0.6829 (tm-30)
REVERT: B  910 ASP cc_start: 0.5389 (t0) cc_final: 0.5132 (t0)
REVERT: B  975 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7784 (ptmm)
REVERT: B 1061 ARG cc_start: 0.6726 (mtm-85) cc_final: 0.5965 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6414 (mtm-85) cc_final: 0.6086 (mtm-85)
REVERT: B 1106 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6517 (mp10)
REVERT: B 1175 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6284 (mtm-85)
REVERT: B 1226 LYS cc_start: 0.7414 (pttm) cc_final: 0.6916 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7475 (p0) cc_final: 0.7044 (p0)
REVERT: B 1265 ASN cc_start: 0.7900 (m-40) cc_final: 0.7673 (m110)
REVERT: B 1282 TRP cc_start: 0.7445 (m100) cc_final: 0.7032 (m100)
  outliers start: 22
  outliers final: 14
  residues processed: 147
  average time/residue: 1.1932
  time to fit residues: 186.2009
Evaluate side-chains
  145 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  646 ASN
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  944 SER
Chi-restraints excluded: chain B residue  975 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1106 GLN
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1209 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 91 optimal weight:    5.9990
   chunk 96 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0970
   overall best weight:    0.9380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.220188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.140558 restraints weight = 8977.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 2.58
r_work: 0.3479 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8388  Z= 0.146
  Angle     :  0.572  11.757  11350  Z= 0.297
  Chirality :  0.044   0.283   1244
  Planarity :  0.003   0.029   1428
  Dihedral  :  4.979  45.275   1221
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.86 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.27), residues: 1006
  helix:  2.11 (0.25), residues: 414
  sheet:  0.26 (0.34), residues: 224
  loop : -1.08 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B1266 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.019   0.001   PHE A 512 
 TYR   0.028   0.001   TYR B1133 
 ARG   0.007   0.000   ARG B 903 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00389 (    3)
  link_NAG-ASN         : angle       2.89679 (    9)
  link_BETA1-4         : bond        0.00650 (    1)
  link_BETA1-4         : angle       1.22577 (    3)
  hydrogen bonds       : bond        0.05000 (  374)
  hydrogen bonds       : angle       4.44228 ( 1077)
  link_BETA1-6         : bond        0.00458 (    1)
  link_BETA1-6         : angle       1.18871 (    3)
  covalent geometry    : bond        0.00339 ( 8383)
  covalent geometry    : angle       0.56582 (11335)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.7098 (mtm110)
REVERT: A  158 GLU cc_start: 0.7481 (tt0) cc_final: 0.7194 (tt0)
REVERT: A  197 MET cc_start: 0.6596 (mtm) cc_final: 0.5043 (tpt)
REVERT: A  366 LYS cc_start: 0.7282 (mtmt) cc_final: 0.6645 (mttm)
REVERT: A  372 MET cc_start: 0.7535 (mtm) cc_final: 0.7058 (mmp)
REVERT: A  444 ARG cc_start: 0.7002 (ttp-110) cc_final: 0.6494 (ttt180)
REVERT: A  491 ARG cc_start: 0.7493 (tmt170) cc_final: 0.7074 (tpt-90)
REVERT: A  522 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7543 (tppt)
REVERT: A  535 TYR cc_start: 0.8577 (t80) cc_final: 0.8315 (t80)
REVERT: A  563 GLU cc_start: 0.8172 (pt0) cc_final: 0.7761 (tp30)
REVERT: A  570 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6978 (mtm110)
REVERT: A  581 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7301 (mm-30)
REVERT: A  742 GLN cc_start: 0.7067 (tm130) cc_final: 0.6787 (tm-30)
REVERT: B  910 ASP cc_start: 0.5421 (t0) cc_final: 0.5218 (t0)
REVERT: B  975 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7905 (ptmm)
REVERT: B 1061 ARG cc_start: 0.6652 (mtm-85) cc_final: 0.5916 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6385 (mtm-85) cc_final: 0.6039 (mtm-85)
REVERT: B 1106 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6592 (mp10)
REVERT: B 1175 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6328 (mtm-85)
REVERT: B 1246 ASP cc_start: 0.7506 (p0) cc_final: 0.7088 (p0)
REVERT: B 1265 ASN cc_start: 0.7913 (m-40) cc_final: 0.7693 (m110)
REVERT: B 1282 TRP cc_start: 0.7464 (m100) cc_final: 0.7000 (m100)
  outliers start: 24
  outliers final: 15
  residues processed: 138
  average time/residue: 1.2838
  time to fit residues: 188.3510
Evaluate side-chains
  143 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  522 LYS
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  975 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1074 LEU
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1106 GLN
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 87 optimal weight:    5.9990
   chunk 94 optimal weight:    0.0770
   chunk 51 optimal weight:    0.0980
   chunk 83 optimal weight:    2.9990
   chunk 98 optimal weight:   10.0000
   chunk 74 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 55 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.4538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.222618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.143677 restraints weight = 9052.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.60
r_work: 0.3495 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8388  Z= 0.117
  Angle     :  0.556  13.193  11350  Z= 0.288
  Chirality :  0.043   0.255   1244
  Planarity :  0.003   0.033   1428
  Dihedral  :  4.617  42.277   1221
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.43 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.27), residues: 1006
  helix:  2.24 (0.25), residues: 416
  sheet:  0.35 (0.34), residues: 224
  loop : -1.03 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B1266 
 HIS   0.003   0.000   HIS A 494 
 PHE   0.015   0.001   PHE A 516 
 TYR   0.020   0.001   TYR B1133 
 ARG   0.008   0.000   ARG B 903 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00451 (    3)
  link_NAG-ASN         : angle       2.37684 (    9)
  link_BETA1-4         : bond        0.00633 (    1)
  link_BETA1-4         : angle       1.34555 (    3)
  hydrogen bonds       : bond        0.04308 (  374)
  hydrogen bonds       : angle       4.31316 ( 1077)
  link_BETA1-6         : bond        0.00505 (    1)
  link_BETA1-6         : angle       1.16781 (    3)
  covalent geometry    : bond        0.00257 ( 8383)
  covalent geometry    : angle       0.55177 (11335)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7079 (mtm110)
REVERT: A  158 GLU cc_start: 0.7512 (tt0) cc_final: 0.7263 (tt0)
REVERT: A  197 MET cc_start: 0.6568 (mtm) cc_final: 0.4944 (tmm)
REVERT: A  366 LYS cc_start: 0.7237 (mtmt) cc_final: 0.6688 (mttm)
REVERT: A  372 MET cc_start: 0.7537 (mtm) cc_final: 0.7069 (mmp)
REVERT: A  382 MET cc_start: 0.6839 (mmt) cc_final: 0.6500 (mpt)
REVERT: A  444 ARG cc_start: 0.7062 (ttp-110) cc_final: 0.6538 (ttt180)
REVERT: A  491 ARG cc_start: 0.7507 (tmt170) cc_final: 0.7094 (tpt-90)
REVERT: A  535 TYR cc_start: 0.8557 (t80) cc_final: 0.8251 (t80)
REVERT: A  563 GLU cc_start: 0.8180 (pt0) cc_final: 0.7789 (tp30)
REVERT: A  581 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7366 (mm-30)
REVERT: A  742 GLN cc_start: 0.7071 (tm130) cc_final: 0.6792 (tm-30)
REVERT: B  910 ASP cc_start: 0.5570 (t0) cc_final: 0.5355 (t0)
REVERT: B  975 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7828 (ptmm)
REVERT: B 1061 ARG cc_start: 0.6670 (mtm-85) cc_final: 0.5912 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6391 (mtm-85) cc_final: 0.6051 (mtm-85)
REVERT: B 1175 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6289 (mtm-85)
REVERT: B 1246 ASP cc_start: 0.7545 (p0) cc_final: 0.7180 (p0)
REVERT: B 1265 ASN cc_start: 0.7906 (m-40) cc_final: 0.7681 (m110)
REVERT: B 1282 TRP cc_start: 0.7422 (m100) cc_final: 0.7034 (m100)
  outliers start: 24
  outliers final: 14
  residues processed: 137
  average time/residue: 1.1543
  time to fit residues: 168.0411
Evaluate side-chains
  135 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 ARG
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  975 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1116 LEU
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 83 optimal weight:    0.1980
   chunk 80 optimal weight:    7.9990
   chunk 85 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 86 optimal weight:    0.5980
   chunk 92 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.221500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.142650 restraints weight = 8799.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.55
r_work: 0.3500 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8388  Z= 0.129
  Angle     :  0.558  12.142  11350  Z= 0.289
  Chirality :  0.043   0.258   1244
  Planarity :  0.003   0.029   1428
  Dihedral  :  4.513  41.687   1221
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 19.23 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.27), residues: 1006
  helix:  2.25 (0.25), residues: 415
  sheet:  0.33 (0.34), residues: 224
  loop : -1.08 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B1266 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.017   0.001   PHE A 512 
 TYR   0.018   0.001   TYR B1133 
 ARG   0.005   0.000   ARG B 903 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00406 (    3)
  link_NAG-ASN         : angle       2.40264 (    9)
  link_BETA1-4         : bond        0.00652 (    1)
  link_BETA1-4         : angle       1.37466 (    3)
  hydrogen bonds       : bond        0.04510 (  374)
  hydrogen bonds       : angle       4.33232 ( 1077)
  link_BETA1-6         : bond        0.00492 (    1)
  link_BETA1-6         : angle       1.17291 (    3)
  covalent geometry    : bond        0.00296 ( 8383)
  covalent geometry    : angle       0.55397 (11335)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7079 (mtm110)
REVERT: A  158 GLU cc_start: 0.7557 (tt0) cc_final: 0.7298 (tt0)
REVERT: A  197 MET cc_start: 0.6571 (mtm) cc_final: 0.4964 (tmm)
REVERT: A  366 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6739 (mttm)
REVERT: A  372 MET cc_start: 0.7518 (mtm) cc_final: 0.7042 (mmp)
REVERT: A  382 MET cc_start: 0.6837 (mmt) cc_final: 0.6463 (mpt)
REVERT: A  444 ARG cc_start: 0.7072 (ttp-110) cc_final: 0.6563 (ttt180)
REVERT: A  491 ARG cc_start: 0.7456 (tmt170) cc_final: 0.7062 (tpt-90)
REVERT: A  522 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7531 (ttpp)
REVERT: A  535 TYR cc_start: 0.8576 (t80) cc_final: 0.8352 (t80)
REVERT: A  563 GLU cc_start: 0.8194 (pt0) cc_final: 0.7822 (tp30)
REVERT: A  581 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7377 (mm-30)
REVERT: A  742 GLN cc_start: 0.7103 (tm130) cc_final: 0.6885 (tm-30)
REVERT: B  975 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7764 (ptmm)
REVERT: B 1061 ARG cc_start: 0.6670 (mtm-85) cc_final: 0.5903 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6376 (mtm-85) cc_final: 0.6034 (mtm-85)
REVERT: B 1219 GLN cc_start: 0.7264 (pt0) cc_final: 0.5937 (pp30)
REVERT: B 1246 ASP cc_start: 0.7566 (p0) cc_final: 0.7205 (p0)
REVERT: B 1265 ASN cc_start: 0.7861 (m-40) cc_final: 0.7656 (m110)
REVERT: B 1282 TRP cc_start: 0.7431 (m100) cc_final: 0.7038 (m100)
  outliers start: 17
  outliers final: 15
  residues processed: 129
  average time/residue: 1.2370
  time to fit residues: 169.2416
Evaluate side-chains
  136 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 ARG
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  975 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1116 LEU
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9980
   chunk 93 optimal weight:   20.0000
   chunk 69 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 60 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 913 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.220899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.145442 restraints weight = 8978.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 3.07
r_work: 0.3467 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8388  Z= 0.133
  Angle     :  0.559  11.839  11350  Z= 0.290
  Chirality :  0.043   0.260   1244
  Planarity :  0.003   0.029   1428
  Dihedral  :  4.460  42.052   1221
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.00 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.27), residues: 1006
  helix:  2.21 (0.25), residues: 415
  sheet:  0.30 (0.34), residues: 225
  loop : -1.06 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B1266 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.014   0.001   PHE A 516 
 TYR   0.018   0.001   TYR B1133 
 ARG   0.010   0.000   ARG B 903 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00381 (    3)
  link_NAG-ASN         : angle       2.34451 (    9)
  link_BETA1-4         : bond        0.00683 (    1)
  link_BETA1-4         : angle       1.31001 (    3)
  hydrogen bonds       : bond        0.04675 (  374)
  hydrogen bonds       : angle       4.33478 ( 1077)
  link_BETA1-6         : bond        0.00411 (    1)
  link_BETA1-6         : angle       1.13698 (    3)
  covalent geometry    : bond        0.00304 ( 8383)
  covalent geometry    : angle       0.55510 (11335)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8573.86 seconds
wall clock time: 147 minutes 32.16 seconds (8852.16 seconds total)